"Fearful Symmetry" (ep 6): You've got to figure that at least a third of the Justice League already owes their origin to some government project or another. (Or does that only happen in the Marvel universe?) So the secret conspiracy focuses on... creating yet more superheroes, who will be "loyal" to the government. Good luck with that, guys.
"The Greatest Story Never Told" (ep 7): If you get a black hole embedded in your chest, perhaps you should stay close to the lab where they can help you. Instead of, say, wandering around downtown Metropolis creating (additional) havoc while mumbling apologies for doing so.
"Ultimatum" (ep 9): A 3-fer.
(A) Maybe I have entirely to optimistic a view of police procedures, but I'm pretty sure that the Metropolis police department does not turn over arrested supervillains just because some strangers with high-tech weaponry show up and claim to be from the feds. There's got to be some paperwork involved at least. On the other hand, maybe this explains the DC Universe's high recidivism rate.
(B) Also further evidence that the secret conspiracy is half-baked as the Ultimen learn of their origin, and then defect or rebel.
(C) You don't try to blackmail Batman. When does that ever work out well?